SearcharxivSearch

arXiv subjects

Geoff K. Nicholls

Publications and source records attributed to Geoff K. Nicholls.

At least 19 recordsLinked to original sources

Bessel-Debiased Pseudo-Marginal MCMC for Generalised Bayesian Inference

Generalised Bayesian inference uses weights of the form $\exp\{-\beta_n\ell_n(\theta)\}$ even when the loss is only estimated. Exponentiating an unbiased loss estimate changes the target, and when $\beta_n\asymp n$ an ordinary Monte Carlo loss estimate with variance of order $M^{-1}$ requires a per-proposal budget $M$ of order $n^2$ to keep the leading log-weight variance bounded. We introduce Sign-Corrected Bessel Debiasing (SCBD), a signed pseudo-marginal method based on independent block estimates of the loss, and study its ordinary-MC and independently randomised quasi-Monte Carlo (RQMC) implementations. Under an i.i.d. Gaussian block model, a Bessel factor constructed from the block sample variance exactly removes the Gaussian exponential inflation despite the variance being unknown. For general non-Gaussian finite blocks, the method targets a posterior differing from the intended posterior by a parameter-dependent multiplicative factor. Under regularity conditions, the uncorrected and corrected ordinary-MC targets have total-variation errors of orders $\beta_n^2/M_n$ and $\beta_n^3/M_n^2$. If an RQMC block estimator has variance $\mathcal O\{B^{-\alpha}(\log B)^{d-1}\}$, the corresponding errors are of orders $\delta^{\mathrm{RQ}}_{n,M_n}$ and $(\delta^{\mathrm{RQ}}_{n,M_n})^{3/2}$, where $\delta^{\mathrm{RQ}}_{n,M_n}=\beta_n^2M_n^{-\alpha}{\log(2+M_n)}^{d-1}$. The same variance rate gives a sufficient budget of order $n^{2/\alpha}$, up to logarithmic factors, for bounded leading log-weight variance when $\beta_n\asymp n$. The numerical examples show that favourable RQMC representations can inherit this budget scaling and that variance reduction and Bessel correction are complementary. Compared to existing exact corrections, Bessel debiasing is essentially "for free". It is generic, easy to code and supported by theory.

stat.CO

Hierarchical Partial-Order Models for Ranking

Rank aggregation combines information from ordered lists ranking items by preference. Classical parametric models for such data, including the Mallows and Plackett-Luce models, assume the orders concentrate around one or more complete consensus rankings. Recent work relaxes the total-order assumption by allowing the consensus structure to be a partial order (poset), allowing for incomparabilities in preferences. However, in many applications preference data exhibit group structure. We introduce hierarchical partial order (HPO) models, which extend poset-based models to accommodate grouped data through a hierarchy of latent posets. This framework, which parallels mixture model extensions of the Mallows and Plackett-Luce models, enables principled sharing of information across groups while preserving partial-order structure. We show that the Plackett-Luce model and its hierarchical variants are special cases of HPO-models. We develop a hierarchical clustering extension (HCPO) for unsupervised clustering in settings where group labels are unknown. Bayesian inference for the latent poset hierarchy is performed using Markov chain Monte Carlo methods. Experiments on synthetic and real-world datasets, including pairwise acoustic preference data and LLM agent traces, demonstrate that the proposed HPO and HCPO models outperform existing approaches in both predictive performance and structural interpretability.

stat.ME

De-Linearizing Agent Traces: Bayesian Inference of Latent Partial Orders for Efficient Execution

AI agents increasingly execute procedural workflows as sequential action traces, which obscures latent concurrency and induces repeated step-by-step reasoning. We introduce BPOP, a Bayesianframework that infers a latent dependency partial order from noisy linearized traces. BPOP models traces as stochastic linear extensions of an underlying graph and performs efficient MCMC inference via a tractable frontier-softmax likelihood that avoids #P-hard marginalization over linear extensions. We evaluate on our open-sourced Cloud-IaC-6, a suite of cloud provisioning tasks with heterogeneous LLM-generated traces, and WFCommons scientific workflows. BPOP recover dependency structure more accurately than trace-only and process-mining baselines, and the inferred graphs support a compiled executor that prunes irrelevant context, yielding substantial reductions in token usage and execution time.

stat.AP

Amortized Simulation-Based Inference in Generalized Bayes via Neural Posterior Estimation

Generalized Bayesian Inference (GBI) tempers a loss with a temperature $β> 0$ to mitigate overconfidence and improve robustness under model misspecification, but existing GBI methods typically rely on costly MCMC or SDE-based samplers and must be re-run for each new dataset and each $β$ value. We give the first fully amortized variational approximation for the tempered posterior family by training a single data- and $β$-conditioned neural posterior estimator that enables sampling in a single forward pass, without simulator calls or inference-time MCMC. We introduce two complementary training routes: one synthesizes off-manifold samples from the tempered joint distribution, and the other reweights a fixed base dataset using self-normalized importance sampling (SNIS). We show that the SNIS-weighted objective provides a consistent forward-KL fit to the tempered posterior with finite weight variance. Across four standard simulation-based inference benchmarks, including the chaotic Lorenz-96 system, our $β$-amortized estimator achieves competitive posterior approximations, in standard two-sample metrics, matching non-amortized MCMC-based power-posterior samplers over a wide range of temperatures.

stat.ML

Bayesian inference for the learning rate in Generalised Bayesian inference

In Generalised Bayesian Inference (GBI), the learning rate and hyperparameters of the loss must be estimated. These inference-hyperparameters can't be estimated jointly with the other parameters, from the data, by giving them a prior. However, in some settings there exist unknown ``true'' hyperparameter-values about which it is meaningful to have prior belief. It is then possible to use Bayesian inference with held-out data to get hyperparameter-posteriors. We define two hyperparameter posteriors, one based on an ELPPD-utility and one aiming to cover the pseudo-true parameter. The new framework supports estimation and uncertainty quantification for multiple hyperparameters jointly. Experiments show that the resulting GBI-posteriors out-perform Bayesian inference on simulated test data and select optimal or near optimal hyperparameter values in a large real problem of text analysis. Generalised Bayesian inference is particularly useful for combining multiple data sets and most of our examples belong to that setting. We also give asymptotic results for some of the special ``multi-modular'' Generalised Bayes posteriors which we use in our examples.

stat.ME

A Differentiable Bayesian Relaxation for Latent Partial-Order Inference

Many ranking and agent trace datasets are recorded as linear orders even though their latent structure is only partially ordered. This is especially common in agent and workflow traces, where observed order may reflect arbitrary linearization rather than true prerequisites. We introduce a differentiable relaxation for latent partial-order inference from such traces. Starting from a hard frontier-constrained model of noisy linear extensions, we replace discontinuous product-order precedence and binary frontier feasibility with smooth surrogates, yielding a continuous posterior that preserves closure-level partial-order semantics and supports gradient-based MCMC and variational inference. We prove soft transitivity, sharp-limit frontier recovery, and convergence to the hard likelihood. Experiments on synthetic data, records of social dominance relations, and cloud-agent traces show close posterior fidelity to hard MCMC on small instances and improved runtime--accuracy trade-offs on larger problems.

stat.ML

Amortising over hyperparameters in Generalised Bayesian Inference

In Bayesian inference prior hyperparameters are chosen subjectively or estimated using empirical Bayes methods. Generalised Bayesian Inference (GBI) also has a learning rate hyperparameter. This is compounded in Semi-Modular Inference (SMI), a GBI framework for multiple datasets (multi-modular problems). As part of any GBI workflow it is necessary to check sensitivity to the choice of hyperparameters, but running MCMC or fitting a variational approximation at each of the hyperparameter values of interest is impractical. Simulation-based Inference has been used by previous authors to amortise over data and hyperparameters, fitting a posterior approximation targeting the forward-KL divergence. However, for GBI and SMI posteriors, it is not possible to amortise over data, as there is no generative model. Working with a variational family parameterised by a conditional normalising flow, we give a direct variational approximation for GBI and SMI posteriors, targeting the reverse-KL divergence, and amortised over prior and loss hyperparameters at fixed data. This can be sampled efficiently at different hyperparameter values without refitting, and supports efficient robustness checks and hyperparameter selection. We show that there exist amortised conditional normalising-flow architectures which are universal approximators. We illustrate our methods with an epidemiological example well known in SMI work and then give the motivating application, a spatial location-prediction task for linguistic-profile data. SMI gives improved prediction with hyperparameters chosen using our amortised framework. The code is available online.

stat.CO

Simultaneous Reconstruction of Spatial Frequency Fields and Sample Locations via Bayesian Semi-Modular Inference

Traditional methods for spatial inference estimate smooth interpolating fields based on features measured at well-located points. When the spatial locations of some observations are missing, joint inference of the fields and locations is possible as the fields inform the locations and vice versa. If the number of missing locations is large, conventional Bayesian Inference fails if the generative model for the data is even slightly mis-specified, due to feedback between estimated fields and the imputed locations. Semi-Modular Inference (SMI) offers a solution by controlling the feedback between different modular components of the joint model using a hyper-parameter called the influence parameter. Our work is motivated by linguistic studies on a large corpus of late-medieval English textual dialects. We simultaneously learn dialect fields using dialect features observed in ``anchor texts'' with known location and estimate the location of origin for ``floating'' textual dialects of unknown origin. The optimal influence parameter minimises a loss measuring the accuracy of held-out anchor data. We compute a (flow-based) variational approximation to the SMI posterior for our model. This allows efficient computation of the optimal influence. MCMC-based approaches, feasible on small subsets of the data, are used to check the variational approximation.

stat.AP

Exploring Learning Rate Selection in Generalised Bayesian Inference using Posterior Predictive Checks

Generalised Bayesian Inference (GBI) attempts to address model misspecification in a standard Bayesian setup by tempering the likelihood. The likelihood is raised to a fractional power, called the learning rate, which reduces its importance in the posterior and has been established as a method to address certain kinds of model misspecification. Posterior Predictive Checks (PPC) attempt to detect model misspecification by locating a diagnostic, computed on the observed data, within the posterior predictive distribution of the diagnostic. This can be used to construct a hypothesis test where a small $p$-value indicates potential misfit. The recent Embedded Diachronic Sense Change (EDiSC) model suffers from misspecification and benefits from likelihood tempering. Using EDiSC as a case study, this exploratory work examines whether PPC could be used in a novel way to set the learning rate in a GBI setup. Specifically, the learning rate selected is the lowest value for which a hypothesis test using the log likelihood diagnostic is not rejected at the 10% level. The experimental results are promising, though not definitive, and indicate the need for further research along the lines suggested here.

stat.ME

Bayesian inference for partial orders from random linear extensions: power relations from 12th Century Royal Acta

In the eleventh and twelfth centuries in England, Wales and Normandy, Royal Acta were legal documents in which witnesses were listed in order of social status. Any bishops present were listed as a group. For our purposes, each witness-list is an ordered permutation of bishop names with a known date or date-range. Changes over time in the order bishops are listed may reflect changes in their authority. Historians would like to detect and quantify these changes. There is no reason to assume that the underlying social order which constrains bishop-order within lists is a complete order. We therefore model the evolving social order as an evolving partial ordered set or {\it poset}. We construct a Hidden Markov Model for these data. The hidden state is an evolving poset (the evolving social hierarchy) and the emitted data are random total orders (dated lists) respecting the poset present at the time the order was observed. This generalises existing models for rank-order data such as Mallows and Plackett-Luce. We account for noise via a random ``queue-jumping'' process. Our latent-variable prior for the random process of posets is marginally consistent. A parameter controls poset depth and actor-covariates inform the position of actors in the hierarchy. We fit the model, estimate posets and find evidence for changes in status over time. We interpret our results in terms of court politics. Simpler models, based on Bucket Orders and vertex-series-parallel orders, are rejected. We compare our results with a time-series extension of the Plackett-Luce model. Our software is publicly available.

stat.ME

Non-Parametric Bayesian Inference for Partial Orders with Ties from Rank Data observed with Mallows Noise

Partial orders may be used for modeling and summarising ranking data when the underlying order relations are less strict than a total order. They are a natural choice when the data are lists recording individuals' positions in queues in which queue order is constrained by a social hierarchy, as it may be appropriate to model the social hierarchy as a partial order and the lists as random linear extensions respecting the partial order. In this paper, we set up a new prior model for partial orders incorporating ties by clustering tied actors using a Poisson Dirichlet process. The family of models is projective. We perform Bayesian inference with different choices of noisy observation model. In particular, we propose a Mallow's observation model for our partial orders and give a recursive likelihood evaluation algorithm. We demonstrate our model on the 'Royal Acta' (Bishop) list data where we find the model is favored over well-known alternatives which fit only total orders.

stat.ME

An Embedded Diachronic Sense Change Model with a Case Study from Ancient Greek

Word meanings change over time, and word senses evolve, emerge or die out in the process. For ancient languages, where the corpora are often small and sparse, modelling such changes accurately proves challenging, and quantifying uncertainty in sense-change estimates consequently becomes important. GASC (Genre-Aware Semantic Change) and DiSC (Diachronic Sense Change) are existing generative models that have been used to analyse sense change for target words from an ancient Greek text corpus, using unsupervised learning without the help of any pre-training. These models represent the senses of a given target word such as "kosmos" (meaning decoration, order or world) as distributions over context words, and sense prevalence as a distribution over senses. The models are fitted using Markov Chain Monte Carlo (MCMC) methods to measure temporal changes in these representations. This paper introduces EDiSC, an Embedded DiSC model, which combines word embeddings with DiSC to provide superior model performance. It is shown empirically that EDiSC offers improved predictive accuracy, ground-truth recovery and uncertainty quantification, as well as better sampling efficiency and scalability properties with MCMC methods. The challenges of fitting these models are also discussed.

cs.CL

Biclustering random matrix partitions with an application to classification of forensic body fluids

Classification of unlabeled data is usually achieved by supervised learning from labeled samples. Although there exist many sophisticated supervised machine learning methods that can predict the missing labels with a high level of accuracy, they often lack the required transparency in situations where it is important to provide interpretable results and meaningful measures of confidence. Body fluid classification of forensic casework data is the case in point. We develop a new Biclustering Dirichlet Process for Class-assignment with Random Matrices (BDP-CaRMa), with a three-level hierarchy of clustering, and a model-based approach to classification that adapts to block structure in the data matrix. As the class labels of some observations are missing, the number of rows in the data matrix for each class is unknown. BDP-CaRMa handles this and extends existing biclustering methods by simultaneously biclustering multiple matrices each having a randomly variable number of rows. We demonstrate our method by applying it to the motivating problem, which is the classification of body fluids based on mRNA profiles taken from crime scenes. The analyses of casework-like data show that our method is interpretable and produces well-calibrated posterior probabilities. Our model can be more generally applied to other types of data with a similar structure to the forensic data.

stat.ME

TraitLab: a Matlab package for fitting and simulating binary tree-like data

TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits are simultaneously lost while new ones arise, and borrowing, whereby traits transfer laterally between species as well as through ancestral relationships. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distribution for tree topologies, clade and root ages, and the trait loss, catastrophe and borrowing rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for heterogeneity in the trait loss rate, biases in the data collection process and borrowing of traits between lineages. Coupled pairs of Markov chains can be used to diagnose MCMC mixing and convergence and to debias MCMC estimators. The raw data, MCMC run output, and model fit can be inspected using a number of useful graphical and analytical tools provided within the package or imported into other popular analysis programs. TraitLab is freely available and runs within the Matlab computing environment with its Statistics and Machine Learning toolbox, no other additional toolboxes are required.

stat.CO

Bayesian Inference for Vertex-Series-Parallel Partial Orders

Partial orders are a natural model for the social hierarchies that may constrain "queue-like" rank-order data. However, the computational cost of counting the linear extensions of a general partial order on a ground set with more than a few tens of elements is prohibitive. Vertex-series-parallel partial orders (VSPs) are a subclass of partial orders which admit rapid counting and represent the sorts of relations we expect to see in a social hierarchy. However, no Bayesian analysis of VSPs has been given to date. We construct a marginally consistent family of priors over VSPs with a parameter controlling the prior distribution over VSP depth. The prior for VSPs is given in closed form. We extend an existing observation model for queue-like rank-order data to represent noise in our data and carry out Bayesian inference on "Royal Acta" data and Formula 1 race data. Model comparison shows our model is a better fit to the data than Plackett-Luce mixtures, Mallows mixtures, and "bucket order" models and competitive with more complex models fitting general partial orders.

stat.ME

Scalable Semi-Modular Inference with Variational Meta-Posteriors

The Cut posterior and related Semi-Modular Inference are Generalised Bayes methods for Modular Bayesian evidence combination. Analysis is broken up over modular sub-models of the joint posterior distribution. Model-misspecification in multi-modular models can be hard to fix by model elaboration alone and the Cut posterior and SMI offer a way round this. Information entering the analysis from misspecified modules is controlled by an influence parameter $η$ related to the learning rate. This paper contains two substantial new methods. First, we give variational methods for approximating the Cut and SMI posteriors which are adapted to the inferential goals of evidence combination. We parameterise a family of variational posteriors using a Normalising Flow for accurate approximation and end-to-end training. Secondly, we show that analysis of models with multiple cuts is feasible using a new Variational Meta-Posterior. This approximates a family of SMI posteriors indexed by $η$ using a single set of variational parameters.

stat.ML

Valid belief updates for prequentially additive loss functions arising in Semi-Modular Inference

Model-based Bayesian evidence combination leads to models with multiple parameteric modules. In this setting the effects of model misspecification in one of the modules may in some cases be ameliorated by cutting the flow of information from the misspecified module. Semi-Modular Inference (SMI) is a framework allowing partial cuts which modulate but do not completely cut the flow of information between modules. We show that SMI is part of a family of inference procedures which implement partial cuts. It has been shown that additive losses determine an optimal, valid and order-coherent belief update. The losses which arise in Cut models and SMI are not additive. However, like the prequential score function, they have a kind of prequential additivity which we define. We show that prequential additivity is sufficient to determine the optimal valid and order-coherent belief update and that this belief update coincides with the belief update in each of our SMI schemes.

stat.ME

Tree based credible set estimation

Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and visualisation. There are often two layers of approximation, as we may need to compute a credible set for a target density which is itself only an approximation to the true posterior density. We obtain joint Highest Posterior Density credible sets for density estimation trees given by Li et al. (2016) approximating a density truncated to a compact subset of R^d as this is preferred to a copula construction. These trees approximate a joint posterior distribution from posterior samples using a piecewise constant function defined by sequential binary splits. We use a consistent estimator to measure of the symmetric difference between our credible set estimate and the true HPD set of the target density samples. This quality measure can be computed without the need to know the true set. We show how the true-posterior-coverage of an approximate credible set estimated for an approximate target density may be estimated in doubly intractable cases where posterior samples are not available. We illustrate our methods with simulation studies and find that our estimator is competitive with existing methods.

stat.ME